AIPLAB — Adaptive & Integrated Photonics Lab

Publications

Book chapters

  1. S. Vidic, M.F. Estrada, ,K. Gjerde, V.E. Santo, A. Osswald, M. Barbier, Y.T. Chong, W. SommerGruber, R. de Hoogt, C. Brito, R. Graeser. PREDECT Protocols for Complex 2D/3D Cultures, Chapter in: S.  Ziegler and H. Waldmann (eds.), Systems Chemical Biology, Methods in Molecular Biology 1888, Humana Press, New York, NY (2019)

Journal papers

  1. F.  Molenberghs, M. Verschuuren, M. Barbier, J.J.  Bogers, N. Cools, P. Delputte, M.  Schelhaas, W.H.  De Vos, Cells infected with human papilloma pseudovirus display nuclear reorganization and heterogenous infection kinetics, Cytometry A, 1-14 (2022)

  2. Ü. S. Nizam , G. Makey, M. Barbier, S.S. Kahraman, E. Demir, E.E. Shafigh, S. Galioglu, D. Vahabli, S. Hüsnügil, M.H. Günes, E. Yelesti, S.K. Ilday, Dynamic evolution of hyperuniformity in a driven dissipative colloidal system, J.ournal of Physics: Condensed Matter 33 304002 (2021), doi: 10.1088/1361-648X/abf9b8

  3. J. Molnar, M. Barbier, W.H. De Vos, P. Horvath, An Elastic Energy Minimization Framework for Mean Contour Calculation, PREPRINT: arXiv:1901.02823 (2019)

  4. S. Missault, C. Anckaerts, S. Ahmadoun, I. Blockx, M. Barbier, K. Bielen, D. Shah, S. Kumar-Singh, W. De Vos, A.-M. Van Der Linden, S. Dedeurwaerdere, M. Verhoye, Hypersynchronicity in the default mode-like network in a neurodevelopmental animal model with relevance for schizophrenia, Behavioural brain research 364 303-316 (2019), doi: 10.1016/j.bbr.2019.02.040

  5. R. de Hoogt, M.F. Estrada, S. Vidic, E.J. Davies, A. Osswald, M. Barbier, V.E. Santo, K. Gjerde, H.J.A.A. van Zoggel, S. Blom, M. Dong, K. Närhi, E. Boghaert, C. Brito, Y. Chong, W. Sommergruber, H. van der Kuip, W.M. van Weerden, E.W. Verschuren, J. Hickman, R. Graeser, Protocols and characterization data for 2D, 3D, and slice-based tumor models from the PREDECT project, Scientific Data 4, 170170 (2017)

  6. M. Barbier, A. Bottelbergs, R. Nuydens, A. Ebneth, W.H. De Vos, SliceMap: An Algorithm for Automated Brain Region Annotation, Bioinformatics (2017), doi: 10.1093/bioinformatics/btx658

  7. J.R. Detrez, J.M. Vanderwinden, M. Barbier, M. Verschuuren, R. Nuydens, X. Langlois, J.P. Timmermans, W.H. De Vos, BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes, Bioinformatics 1-3 (2016), doi: 10.1093/bioinformatics/btw515

  8. K. Stock, M. Estrada, V.E. Santo, S. Vidic, K. Gjerde, A. Rudisch, M. Barbier, S.C. Arundkar, I. Selvam, A. Osswald, W. van Weerden, S. Gruenewald, C. Brito, E. Boghaert, M. Oren, Y.T. Chong, R. de Hoogt, W. Sommergruber, R. Graeser, J. Hickman, Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery, Scientific Reports 6, 28951 (2016)

  9. M. Barbier, S. Jaensch, F. Cornelissen, S. Vidic, K. Gjerde, R. De Hoogt, R. Graeser, E. Gustin, Y.T. Chong, Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids, PLoS ONE 11(6): e0156942 (2016)

  10. M. Barbier, G. Papp, and F. M. Peeters, Snake states and Klein tunneling in a graphene Hall bar with a pn-junction, Appl. Phys. Lett. 100, 163121 (2012)

  11. M. Barbier, P. Vasilopoulos, and F. M. Peeters, Single-layer and bilayer graphene superlattices: collimation, additional Dirac points and Dirac lines, Phil. Trans. R. Soc. A 368, 5499 (2010)

  12. M. Barbier, P. Vasilopoulos, and F. M. Peeters, Kronig-Penney model on bilayer graphene: Spectrum and transmission periodic in the strength of the barriers, Phys. Rev. B 82, 235408 (2010).

  13. M. Barbier, P. Vasilopoulos, and F. M. Peeters, Extra Dirac points in the energy spectrum for superlattices on single-layer graphene, Phys. Rev. B 81, 075438 (2010).

  14. M. Barbier, P. Vasilopoulos, F. M. Peeters, and J. M. Pereira Jr, Band structure, density of states, and transmission in graphene bilayer superlattices, AIP Conference Proceedings 1199, pp. 547–548 (2010).

  15. M. Barbier, P. Vasilopoulos, F. M. Peeters, Dirac electrons in a Kronig-Penney potential: Dispersion relation and transmission periodic in the strength of the barriers, Phys. Rev. B 80, 205415 (2009).

  16. M. Barbier, P. Vasilopoulos, F. M. Peeters, and J. M. Pereira Jr, Bilayer graphene with single and multiple electrostatic barriers: Band structure and transmission, Phys. Rev. B 79, 155402 (2009).

  17. M. Barbier, F. M. Peeters, P. Vasilopoulos, and J. M. Pereira Jr, Dirac and Klein-Gordon particles in one-dimensional periodic potentials, Phys. Rev. B 77, 115446 (2008).

Conferences & Workshops

  1. S. Chakrabarti, I. Haggstrom, G. Makey, M. Barbier, Using MATLAB on EGI HPC services, EGI Conference 2022, Prague, Czech Republic (2022 Sep 21 - 23) [part of oral presentation]

  2. G. Makey, M. Barbier, Exploiting HPC using MATLAB on TRUBA, online Mathworks Turkey workshop Scaling Parallel Computing with MATLAB to HPC @ TRUBA, online workshop (2022 Jul 19) [oral presentation]

  3. M. Barbier, J. Molnar, P. Horvath, W.H. De Vos, Ground truth estimation for image segmentation tasks by contour averaging, RBSM 2019, Louvain-la-Neuve, Belgium (2019 Sep 9) [poster]

  4. M. Barbier, H. Maurin, E. Holvoet, R. Nuydens, P.H. Larsen, P. Horvath, W.H. De Vos, Automated brain region recognition in fluorescent tissue slices using deep learning, Quantitative BioImaging conference, Rennes, France (2019 Jan 8 - 11) [poster]

  5. M. Barbier, A. Bottelbergs, R. Nuydens, P.H. Larsen, P. Horvath, W.H. De Vos, A deep learning approach for automated brain region recognition, DeepLearn 2018, 2nd Intern. summer school on deep learning, Genova, Italy (2018 Jul 23 - 27) [poster]

  6. M. Barbier, A. Bottelbergs, R. Nuydens, A. Ebneth, P.H. Larsen, W.H. De Vos, SliceMap: Automated brain region recognition, Neubias 2018 & school for BioImage Analysts 2018 (Neubias COST action), Szeged, Hungary (2018 Jan 27​ - 30) [poster]

  7. M. Barbier, A. Bottelbergs, R. Nuydens, A. Ebneth, W.H. De Vos, SliceMap: Automated brain region recognition, Janssen Phenomics meeting, Beerse, Belgium (2017) [poster]

  8. M. Barbier, A. Bottelbergs, R. Nuydens, A. Ebneth, W. H. De Vos, SliceMap: Automated brain region recognition based on elastic registration and atlas mapping, Neubias 2017, Oeiras-Lisbon, Portugal (2017) [poster]

  9. M. Barbier, A. Bottelbergs, R. Verboven, R. Nuydens, A. Ebneth, W. H. De Vos, Automated brain region recognition based on elastic registration and atlas mapping, Belgian Brain Congress, (2016 Oct 8) [flash talk and poster]

  10. M. Barbier, A. Bottelbergs, R. Verboven, R. Nuydens, A. Ebneth, W.H. De Vos, Automated brain region recognition based on elastic registration and atlas mapping, RBSM 2016, Brussels, Belgium (2016 Sep 8-9) [poster]

  11. M. Barbier, A. Bottelbergs, R. Verboven, R. Nuydens, A. Ebneth, W.H. De Vos, Automated brain region recognition based on elastic registration and atlas mapping, Optical imaging of brain connectivity: from synapses to networks in action, Roscoff, France (2016 Jun 13 ‐ 17) [poster]

  12. M. Barbier, S. Vidic, K. Gjerde, S. Jaensch, R. de Hoogt, R. Graeser, Y.T. Chong How to perform image analysis on 3D fluorescent cell cultures, PREDECT closing meeting in Paris, France (2015 Oct 4 - 6) [oral presentation]

  13. M. Barbier, F. Cornelissen, S. Vidic, K. Gjerde, S. Jaensch, R. Graeser, E. Gustin, Y.T. Chong, 2.5D image analysis of fluorescent 3D tumor spheroid cultures, PREDECT consortium meeting in Riga, Lithuania (2014 Oct 12 - 14) [poster]

  14. S. Vidic, N. Esser, R. de Hoogt, I. Verberne, I. Kogan-Sakin, Y. Stein, V. Rotter, M. Barbier, Y. Chong, S. De Breucker, K. Smans, M. Akerfelt, M. Nees, P. King, I. Hickson, W. van Weerden, R. Graeser. Complex in vitro and in vivo prostate cancer models for the PREDECT consortium, [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; (2014 Apr 5-9); San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2023. doi:10.1158/1538-7445.AM2014-2023

  15. M. Barbier, F. Cornelissen, S. Vidic, M. Estrada, S. Jaensch, R. Graeser, E. Gustin, Y.T. Chong, 3D image analysis of fluorescent confocal microscopy images of in vitro 3D tumor spheroid cultures, PREDECT consortium meeting in Lisbon, Portugal (2013 Nov 24 - 26) [poster]

  16. M. Barbier, Y.T. Chong, R. Graeser, S. Vidic, R. de Hoogt, S. Jaensch, Fluorescent image analysis of 3D co-cultures, PREDECT consortium plenary meeting in Berlin, Germany (2013 Mar 18 - 21) [oral presentation]

  17. M. Barbier, G. Papp, F. M. Peeters, Effect of skipping and snake orbits on the transport in a graphene Hall bar with a pn-junction, Graphene Week 2012 in Delft, the Netherlands (2012 Jun 3 - 8) [poster]

  18. M. Barbier, F. M. Peeters, Transport in anti-symmetric gap barriers in bilayer graphene, Core-partners-meeting at IMEC, Leuven, Belgium (2010 Apr 21) [poster]

  19. M. Barbier, P. Vasilopoulos, F. M. Peeters, J. Milton Pereira Jr., Band structure, density of states, and transmission in graphene bilayer multiple barrier structures, Graphene week, Abdus Salam ICTP, Miramare-Trieste, Italy (2008 Aug 25 - 29) [poster]

  20. M. Barbier, F. M. Peeters, P. Vasilopoulos, Electronic structure of a superlattice in bilayer graphene, BPS General Scientific Meeting, Brussels, Belgium (2008 May 21) [poster]

  21. M. Barbier, F. M. Peeters, P. Vasilopoulos, Electronic structure of a superlattice in bilayer graphene, Core-partners-meeting at IMEC, Leuven, Belgium (2008 Apr 23) [poster]

  22. M. Barbier, F. M. Peeters, P. Vasilopoulos, J. Milton Pereira Jr., Dirac particles in one-dimensional periodic potentials in graphene, IAP-meeting at the University of Liege (2007 Nov 22) [poster]